ERV FAQ: ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?

• Lots of DNA does stuff, whether it is a part of an ERV or not. If you were to point to something and say, "that looks designed for a purpose", you would do better to point at the genes for vision, say, or digestion. ERVs make no sense from the design point of view. Only bits of some ERVs do anything, and what they do is not always helpful. Why are the other bits there, and why are all the other ERVs there, the ones that have no functional bits? Why do they all have all the hallmarks of retroviral integrations? (See "Why do virologists and geneticists think that ERVs come from retroviruses?"). When you look at ERV function in any of the other sections of this FAQ, ask yourself, "Does this make sense as a by-product of retroviral action, or as something designed to meet a specific purpose?"
• It makes sense for evolution to co-opt useful endogenous retroviral DNA. Detrimental elements will be flushed out of the genome by negative selection. Neutral elements will drift, get chopped up and mutated. Useful elements will tend to increase in frequency in the population generation by generation. An ERV that has lost the ability to replicate complete viruses is in the same evolutionary "boat" as all the rest of the organism's genome. It can't replicate via transcription any more - the route used by functional retroviruses. It's "ticket" into the next generation is the same ticket as all the rest of the organism's DNA - to be useful, or if you can't be useful, be lucky, and get replicated along with all of the rest of the organism's DNA.
• Function is often cited as a rationale for common loci between species. This is based on a misunderstanding of how genetics works. Genes and their promoters can exist almost anywhere on any chromosome, and they will work in the same way. There is no inherent functional reason for corresponding loci in two different species. See Aren't the same ERV genetics in the same places in different species because they have to do the same job?
• See also, "ERVs promote the transcription of host DNA. Doesn't this prove they are designed?" and "ERVs are essential in reproduction (syncytin and the formation of the placenta). How can this be?"